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Rojas L, Cabrera-Muñoz A, Espinosa LA, Montané S, Alvarez-Lajonchere L, Mojarena JD, Moya G, Lorenzo J, González LJ, Betzel C, Alonso-Del-Rivero Antigua M. CogiTx1: A novel subtilisin A inhibitor isolated from the sea anemone Condylactis gigantea belonging to the defensin 4 protein family. Biochimie 2023; 213:41-53. [PMID: 37105301 DOI: 10.1016/j.biochi.2023.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/13/2023] [Accepted: 04/24/2023] [Indexed: 04/29/2023]
Abstract
Subtilisin-like enzymes are recognized as key players in many infectious agents. In this context, its inhibitors are very valuable molecular lead compounds for structure based drug discovery and design. Marine invertebrates offer a great source of bioactive molecules, including protease inhibitors. In this work, we describe a new subtilisin inhibitor, from the sea anemone Condylactis gigantea (CogiTx1). CogiTx1 was purified using a combination of cation exchange chromatography, size exclusion chromatography and RP-HPLC chromatography. CogiTx1 it is a protein with 46 amino acid residues, with 4970.44 Da and three disulfide bridges. Is also able to inhibit subtilisin-like enzymes and pancreatic elastase. According to the amino acid sequence, it belongs to the defensin 4 family of proteins. The sequencing showed that CogiTx1 has an amidated C-terminal end, which was confirmed by the presence of the typical -XGR signal for amidation in the protein sequence deduced from the cDNA. This modification was described at protein level for the first time in this family of proteins. CogiTx1 is the first subtilisin inhibitor from the defensin 4 family and accordingly it has a folding consisting primarily in beta-strands in agreement with the analysis by CD and 3D modelling. Therefore, future in-depth functional studies may allow a more detailed characterization and will shed light on structure-function properties.
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Affiliation(s)
- Laritza Rojas
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, PC: 10400, Cuba
| | - Aymara Cabrera-Muñoz
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, PC: 10400, Cuba
| | - Luis A Espinosa
- Center for Genetic Engineering and Biotechnology, Havana, PC:60 200, Cuba
| | - Sergi Montané
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Cerdanyola del Valles, Barcelona, PC:08193, Spain
| | - Luis Alvarez-Lajonchere
- Felipe Poey Natural History Museum, Faculty of Biology, University of Havana, Havana, PC: 10400, Cuba
| | - Jesús D Mojarena
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, PC: 10400, Cuba
| | - Galina Moya
- Center for Genetic Engineering and Biotechnology, Havana, PC:60 200, Cuba
| | - Julia Lorenzo
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Cerdanyola del Valles, Barcelona, PC:08193, Spain
| | - Luis J González
- Center for Genetic Engineering and Biotechnology, Havana, PC:60 200, Cuba
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Department of Chemistry, Universität Hamburg, Hamburg, PC: 20146, Germany
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Pascual Alonso I, Almeida García F, Valdés Tresanco ME, Arrebola Sánchez Y, Ojeda Del Sol D, Sánchez Ramírez B, Florent I, Schmitt M, Avilés FX. Marine Invertebrates: A Promissory Still Unexplored Source of Inhibitors of Biomedically Relevant Metallo Aminopeptidases Belonging to the M1 and M17 Families. Mar Drugs 2023; 21:md21050279. [PMID: 37233473 DOI: 10.3390/md21050279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Proteolytic enzymes, also known as peptidases, are critical in all living organisms. Peptidases control the cleavage, activation, turnover, and synthesis of proteins and regulate many biochemical and physiological processes. They are also involved in several pathophysiological processes. Among peptidases, aminopeptidases catalyze the cleavage of the N-terminal amino acids of proteins or peptide substrates. They are distributed in many phyla and play critical roles in physiology and pathophysiology. Many of them are metallopeptidases belonging to the M1 and M17 families, among others. Some, such as M1 aminopeptidases N and A, thyrotropin-releasing hormone-degrading ectoenzyme, and M17 leucyl aminopeptidase, are targets for the development of therapeutic agents for human diseases, including cancer, hypertension, central nervous system disorders, inflammation, immune system disorders, skin pathologies, and infectious diseases, such as malaria. The relevance of aminopeptidases has driven the search and identification of potent and selective inhibitors as major tools to control proteolysis with an impact in biochemistry, biotechnology, and biomedicine. The present contribution focuses on marine invertebrate biodiversity as an important and promising source of inhibitors of metalloaminopeptidases from M1 and M17 families, with foreseen biomedical applications in human diseases. The results reviewed in the present contribution support and encourage further studies with inhibitors isolated from marine invertebrates in different biomedical models associated with the activity of these families of exopeptidases.
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Affiliation(s)
- Isel Pascual Alonso
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana 10400, Cuba
| | - Fabiola Almeida García
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana 10400, Cuba
| | - Mario Ernesto Valdés Tresanco
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana 10400, Cuba
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Daniel Ojeda Del Sol
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana 10400, Cuba
| | | | - Isabelle Florent
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum National d'Histoire Naturelle, CNRS, CP52, 57 Rue Cuvier, 75005 Paris, France
| | - Marjorie Schmitt
- Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA UMR 7042, 68000 Mulhouse, France
| | - Francesc Xavier Avilés
- Institute for Biotechnology and Biomedicine and Department of Biochemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Enzyme Inhibitors from Gorgonians and Soft Corals. Mar Drugs 2023; 21:md21020104. [PMID: 36827145 PMCID: PMC9963996 DOI: 10.3390/md21020104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/28/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
For decades, gorgonians and soft corals have been considered promising sources of bioactive compounds, attracting the interest of scientists from different fields. As the most abundant bioactive compounds within these organisms, terpenoids, steroids, and alkaloids have received the highest coverage in the scientific literature. However, enzyme inhibitors, a functional class of bioactive compounds with high potential for industry and biomedicine, have received much less notoriety. Thus, we revised scientific literature (1974-2022) on the field of marine natural products searching for enzyme inhibitors isolated from these taxonomic groups. In this review, we present representative enzyme inhibitors from an enzymological perspective, highlighting, when available, data on specific targets, structures, potencies, mechanisms of inhibition, and physiological roles for these molecules. As most of the characterization studies for the new inhibitors remain incomplete, we also included a methodological section presenting a general strategy to face this goal by accomplishing STRENDA (Standards for Reporting Enzymology Data) project guidelines.
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Machin JM, Kantsadi AL, Vakonakis I. The complex of Plasmodium falciparum falcipain-2 protease with an (E)-chalcone-based inhibitor highlights a novel, small, molecule-binding site. Malar J 2019; 18:388. [PMID: 31791339 PMCID: PMC6889325 DOI: 10.1186/s12936-019-3043-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 11/27/2019] [Indexed: 12/03/2022] Open
Abstract
Background Malaria kills over 400,000 people each year and nearly half the world’s population live in at-risk areas. Progress against malaria has recently stalled, highlighting the need for developing novel therapeutics. The parasite haemoglobin degradation pathway, active in the blood stage of the disease where malaria symptoms and lethality manifest, is a well-established drug target. A key enzyme in this pathway is the papain-type protease falcipain-2. Methods The crystallographic structure of falcipain-2 at 3.45 Å resolution was resolved in complex with an (E)-chalcone small-molecule inhibitor. The falcipain-2–(E)-chalcone complex was analysed with reference to previous falcipain complexes and their similarity to human cathepsin proteases. Results The (E)-chalcone inhibitor binds falcipain-2 to the rear of the substrate-binding cleft. This is the first structure of a falcipain protease where the rear of the substrate cleft is bound by a small molecule. In this manner, the (E)-chalcone inhibitor mimics interactions observed in protein-based falcipain inhibitors, which can achieve high interaction specificity. Conclusions This work informs the search for novel anti-malaria therapeutics that target falcipain-2 by showing the binding site and interactions of the medically privileged (E)-chalcone molecule. Furthermore, this study highlights the possibility of chemically combining the (E)-chalcone molecule with an existing active-site inhibitor of falcipain, which may yield a potent and selective compound for blocking haemoglobin degradation by the malaria parasite.
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Affiliation(s)
- Jonathan M Machin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anastassia L Kantsadi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Ioannis Vakonakis
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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Musyoka T, Bishop ÖT. South African Abietane Diterpenoids and Their Analogs as Potential Antimalarials: Novel Insights from Hybrid Computational Approaches. Molecules 2019; 24:E4036. [PMID: 31703388 PMCID: PMC6891524 DOI: 10.3390/molecules24224036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022] Open
Abstract
The hemoglobin degradation process in Plasmodium parasites is vital for nutrient acquisition required for their growth and proliferation. In P. falciparum, falcipains (FP-2 and FP-3) are the major hemoglobinases, and remain attractive antimalarial drug targets. Other Plasmodium species also possess highly homologous proteins to FP-2 and FP-3. Although several inhibitors have been designed against these proteins, none has been commercialized due to associated toxicity on human cathepsins (Cat-K, Cat-L and Cat-S). Despite the two enzyme groups sharing a common structural fold and catalytic mechanism, distinct active site variations have been identified, and can be exploited for drug development. Here, we utilize in silico approaches to screen 628 compounds from the South African natural sources to identify potential hits that can selectively inhibit the plasmodial proteases. Using docking studies, seven abietane diterpenoids, binding strongly to the plasmodial proteases, and three additional analogs from PubChem were identified. Important residues involved in ligand stabilization were identified for all potential hits through binding pose analysis and their energetic contribution determined by binding free energy calculations. The identified compounds present important scaffolds that could be further developed as plasmodial protease inhibitors. Previous laboratory assays showed the effect of the seven diterpenoids as antimalarials. Here, for the first time, we demonstrate that their possible mechanism of action could be by interacting with falcipains and their plasmodial homologs. Dynamic residue network (DRN) analysis on the plasmodial proteases identified functionally important residues, including a region with high betweenness centrality, which had previously been proposed as a potential allosteric site in FP-2.
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Affiliation(s)
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa;
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